Synthesis and Conformational Analysis of Cyclic Homooligomers from Pyranoid ε‐Sugar Amino Acids

New pyranoid ε‐sugar amino acids were designed as building blocks, in which the carboxylic acid and the amine groups were placed in positions C2 and C3 with respect to the tetrahydropyran oxygen atom. By using standard solution‐phase coupling procedures, cyclic homooligomers containing pyranoid ε‐sugar amino acids were synthesized. Conformation analysis was performed by using NMR spectroscopic experiments, FTIR spectroscopic studies, X‐ray analysis, and a theoretical conformation search. These studies reveal that the presence of a methoxy group in the position C4 of the pyran ring produces an important structural change in the cyclodipeptides. When the methoxy groups are present, the structure collapses through interresidue hydrogen bonds between the oxygen atoms of the pyran ring and the amide protons. However, when the cyclodipeptide lacks the methoxy groups, a U‐shape structure is adopted, in which there is a hydrophilic concave face with four oxygen atoms and two amide protons directed toward the center of the cavity. Additionally, we found important evidence of the key role played by weak electrostatic interactions, such as the five‐membered hydrogen‐bonded pseudocycles (C₅) between the amide protons and the ether oxygen atoms, in the conformation equilibrium of the macrocycles and in the cyclization step of the cyclic tetrapeptides.     

Poly(amide ester)s from 2,6-pyridinedicarboxylic acid and ethanolamine derivatives: identification of macrocycles by matrix-assisted laser desorption/ionization mass spectrometry

The influence of the polycondensation pathway and aminoalcohol structure was investigated in the synthesis of poly(amide ester)s by polytransesterification from ethyl pyridine-2,6-dicarboxylate and 2-amino-2-methylpropan-1-ol or the corresponding bis(amide alcohol), or by polycondensation from the diacid dichloride. Both linear and cyclic structures were identified by steric exclusion chromatography (SEC) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). Transesterification led to cyclic oligomers (macrocycles) with 2-14 pyridine moities in the ring whereas polycondensation from the diacid dichloride gave low molecular weight polymers (Mn = 1800) and macrocycles.     

Cyclic homooligomers of furanoid sugar amino acids

Cyclic homooligomers of mannose-derived furanoid sugar amino acid 1 [H-Maa(Bn(2))-OH] were synthesized by using BOP reagent in the presence of DIPEA under dilute conditions that converted the sugar amino acid monomer directly into its cyclic homooligomers 3a and 4a. The glucose-based sugar amino acid 2 [H-Gaa(Bn(2))-OH] under the same reaction conditions gave a bicyclic lactam 5a as the major product. Cyclic homooligomers of 2 were prepared by cyclizing their linear precursors 6 and 7 leading to the formation of cyclic peptides 8a and 9a, respectively. Conformational analysis by NMR and constrained MD studies revealed that all the cyclic products, 3, 4, 8, and 9, had symmetrical structures. The deprotected cyclic trimer of Maa 3b displayed a conformation in which all the C=O and the N-H bonds of the molecule point in opposite directions. In the deprotected cyclic tetramer of Maa 4b, the COs and NHs were in the plane of the ring with the former pointing to outside and the latter inside the ring. The structure of the cyclic Gaa dimer 8b displayed an unusual six-membered intramolecular hydrogen bond between NH(i)() --> C3-O(i)()(-)(1) and a syn orientation between the C2-H and CO. In this molecule, the C2-hydrogens and the COs can be seen on one side of the ring while the NHs point to the other side. Addition of the bicyclic lactam 5b resulted in the influx of Na(+) ions across the lipid bilayer leading to the dissipation of valinomycin-mediated K(+) diffusion potential.     

3-(1-Aminoalkyl)isoxazole-4-carboxylic acids as peptide bond replacements

An orthogonally protected 3-(1-aminoalkyl)isoxazole-4-carboxylic acid has been prepared by 1,3-dipolar cycloaddition of a suitably protected α-aminonitrile oxide with an enaminoester dipolarophile; this protected amino acid has been deprotected and coupled independently at either the C- or N-terminus to produce pseudopeptide segments as peptide mimetics that contain a cis-amide bond replacement.     

Orthogonally protected cyclo-beta-tetrapeptides as solid-supported scaffolds for the synthesis of glycoclusters

Two novel peptide scaffolds, viz. cyclo[(N(alpha)-Alloc)Dpr-beta-Ala-(N(alpha)-Fmoc)Dpr-beta-Ala] (1) and cyclo[(N(alpha)-Alloc)Dpr-alpha-azido-beta-aminopropanoyl-(N(alpha)-Fmoc)Dpr-beta-Ala] (2), composed of orthogonally protected 2,3-diaminopropanoyl (Dpr) and beta-alanyl residues, have been described. Fmoc chemistry on a backbone amide linker derivatized resin has been used for the chain assembly. Selective removal of the 4-methyltrityl (Mtt) and 1-methyl-1-phenylethyl protections (PhiPr) exposes the beta-amino and carboxyl terminus, respectively, and on-resin cyclization then gives the desired orthogonally protected cyclo-beta-tetrapeptides (1 and 2). The alpha-amino groups, bearing the Fmoc and Alloc protections and the azide mask, allow stepwise orthogonal derivatization of these solid-supported cyclo-beta-tetrapeptide cores (1 and 2). This has been demonstrated by attachments of various sugar units [viz., acetyl- or toluoyl-protected carboxymethyl alpha-d-glycopyranosides (13-15) and methyl 6-O-(4-nitrophenoxycarbonyl)-alpha-d-glycopyranosides (22-24)] to obtain diverse di- and trivalent glycoclusters (33-42). Acidolytic release (TFA) from the support, followed by conventional NaOMe-catalyzed transesterification (33-40) or hydrazine-induced acyl substitution in DMF (41 and 42), gives the fully deprotected clusters (43-52) as final products.     

Tetrahydrofuran Calpha-tetrasubstituted amino acids: two consecutive beta-turns in a crystalline linear tripeptide

The synthesis of tetrahydrofuran Calpha-tetrasubstituted amino acids (TAAs) and their effect on the conformation in small peptides are reported. The synthesis starts from the protein amino acid methionine, which is protected at the C and N terminus and converted into the corresponding sulfonium salt by alkylation. Simple base treatment in the presence of an aryl aldehyde leads to the formation of tetrahydrofuran tetrasubstituted Calpha-amino acids in a highly diastereoselective (trans/cis ratio up to 97:3) reaction with moderate to good yields (35-78%) depending on the aldehyde used. Palladium-catalyzed coupling reactions allow a subsequent further functionalization of the TAA. The R,S,S-TAA-Ala dipeptide amide adopts a beta-turn type I conformation, whereas its S,R,S isomer does not. The R,S,S-Gly-TAA-Ala tripeptide amide shows in the solid state and in solution a conformation of two consecutive beta-turn type III structures, stabilized by i+3-->i intramolecular hydrogen bonds.     

Macro-cyclic aramids (2n-AZA[2n]paracyclophane-2n-ones):new intermediates for the synthesis of p-aramids

An easy route to a new class of n-azapara[2ⁿ] cyclophane-n-ones, N-substituted p-oriented cyclic aromatic amide (cycloaramid) oligomers, is described. The bulky diamine, N, N′-di-sec-butyl-p-phenylenediamine is condensed with terephthaloyl dichloride at elevated temperature in o-dichlorobenzene to provide a high yield of N, N′-di-sec-butyl-p-phenyleneterephthalamide cyclic oligomers (from dimer to tridecamer). The cyclization is favored by the cis conformation of the N-substituted amide bonds present in the growing chain. Ring opening polymerization of these new cycloaramids to high molecular weight linear polymers can be effected in the melt phase with highly nucleophilic catalysts, such as 1,3-dialkylimidazole-2-thiones especially when an acid cocatalyst is employed. The N-substituted polymers yield crystalline films and fibers with an axial repeat length which can only be explained by an unexpected trans conformation of the amide bonds. The facile synthesis of other macrocyclic amides by the steric control of macrocyclization by N-substitution of the amide bond is also described.     

Exploring the conformational and biological versatility of β-turn-modified gramicidin S by using sugar amino acid homologues that vary in ring size

Monobenzylated sugar amino acids (SAAs) that differ in ether ring size (containing an oxetane, furanoid, and pyranoid ring) were synthesized and incorporated in one of the β-turn regions of the cyclo-decapeptide gramicidin S (GS). CD, NMR spectroscopy, modeling, and X-ray diffraction reveal that the ring size of the incorporated SAA moieties determines the spatial positioning of their cis-oriented carboxyl and aminomethyl substituents, thereby subtly influencing the amide linkages with the adjacent amino acids in the sequence. Unlike GS itself, the conformational behavior of the SAA-containing peptides is solvent dependent. The derivative containing the pyranoid SAA is slightly less hydrophobic and displays a diminished haemolytic activity, but has similar antimicrobial properties as GS.     

Folding propensity of cyclohexylether-delta-peptides

[structure: see text] Linear (n = 2-18) and cyclic oligomers (n = 3-8) of a cyclohexylether-delta-amino acid (COA) were prepared in high yield and stereopurity. CD spectra of the linear oligomers were indicative of secondary structure formation. X-ray crystal structures of cyclic COA oligomers revealed hydrophobic packing and internal 5- and 10-membered-ring hydrogen bonds. Ether and amide oxygens reside preferably in an ap orientation. This conformational locking is apparently broken by a C-2 substituent in an asymmetric cyclotrimer, for which a zeolithe-like tubular structure was found.     

Non-aggregational aromatic oligoamide macrocycles

Attaching peripheral amide groups to the backbone of cyclic aromatic oligoamides 1 leads to new macrocycles 2 that show drastically changed behavior including modest yields of formation and no tendency to aggregate while maintaining a rigid backbone and a defined, guest-binding internal cavity.     

New oxazole-based peptidomimetics: useful building blocks for the synthesis of orthogonally protected macrocyclic scaffolds

[structure: see text] The synthesis of a new family of densely functionalized oxazole-containing amino acids is described. These building blocks were employed for preparing macrocycles containing Lys and Glu residues by a combination of solid- and solution-phase synthesis. The resulting structures are presented as orthogonally protected scaffolds for supramolecular chemistry.     

Stereoselective synthesis of orthogonally protected alpha-methylnorlanthionine

[reaction: see text] As the unusual amino acid norlanthionine (nor-Lan) has previously been incorporated into cyclic peptide analogues of the ring C of lantibiotic nisin, we report here the stereoselective synthesis of the new (S,R)- and (R,R)-alpha-methylnorlanthionines (alpha-Me-nor-Lan). The orthogonally protected derivatives of these compounds have also been prepared. The key step in the synthesis of these bisamino acids was the S(N)2 opening reaction of the corresponding cyclic sulfamidates with the SH group of appropriately protected l-cysteine derivatives.     

Simultaneous parallel and antiparallel self-assembly in a triazole/amide macrocycle conformationally homologous to D-,L-α-amino acid based cyclic peptides: NMR and molecular modeling study

A 1,4-linked triazole/amide based peptidomimetic macrocycle, synthesized from a triazole amide oligomer of cis-furanoid sugar triazole amino acids, possesses a conformation resembling the D-,L-α-amino acid based cyclic peptides despite having uniform backbone chirality. It undergoes a unique mode of self-assembly through an antiparallel backbone to backbone intermolecular H-bonding involving amide NH and triazole N2/N3 as well as parallel stacking via amide NH and carbonyl oxygen H-bonding, leading to the formation of a tubular nanostructure.     

Accessing Improbable Foldamer Shapes with Strained Macrocycles

The alkylation of some secondary amide functions with a dimethoxybenzyl (DMB) group in oligomers of 8-amino-2-quinolinecarboxylic acid destabilizes the otherwise favored helical conformations, and allows for cyclization to take place. A cyclic hexamer and a cyclic heptamer were produced in this manner. After DMB removal, X-ray crystallography and NMR show that the macrocycles adopt strained conformations that would be improbable in noncyclic species. The high helix folding propensity of the main chain is partly expressed in these conformations, but it remains frustrated by macrocyclization. Despite being homomeric, the macrocycles possess inequivalent monomer units. Experimental and computational studies highlight specific fluxional pathways within these structures. Extensive simulated annealing molecular dynamics allow for the prediction of the conformations for larger macrocycles with up to sixteen monomers.     

CyClick Chemistry for the Synthesis of Cyclic Peptides

Here, we report a novel “CyClick” strategy for the macrocyclization of peptides that works in an exclusively intramolecular fashion thereby precluding the formation of dimers and oligomers via intermolecular reactions. The CyClick chemistry is highly chemoselective for the N‐terminus of the peptide with a C‐terminal aldehyde. In this protocol, the peptide conformation internally directs activation of the backbone amide bond and thereby facilitates formation of a stable 4‐imidazolidinone‐fused cyclic peptide with high diastereoselectivity (>99 %). This method is tolerant to a variety of peptide aldehydes and has been applied for the synthesis of 12‐ to 23‐membered rings with varying amino acid compositions in one pot under mild reaction conditions. The reaction generated peptide macrocycles featuring a 4‐imidazolidinone in their scaffolds, which acts as an endocyclic control element that promotes intramolecular hydrogen bonding and leads to macrocycles with conformationally rigid turn structures.     

Preparation and unique circular dichroism phenomena of urea-functionalized self-folding resorcinarenes bearing chiral termini through asymmetric hydrogen-bonding belts

Chiral macrocycles with eight (R)- and (S)-methylbenzylurea residues on the resorcinarene skeleton linked through a hexyl or dodecyl spacer having amide linkages have been prepared by the reactions of the corresponding octaamine derivative with (R)- and (S)-alpha-methylbenzylisocyanate, respectively. In chloroform, the urea-functionalized resorcinarenes with hexyl spacers form intramolecular hydrogen bonds by bundling the urea and amide residues in a cyclic fashion to give a self-folding cavitand. The urea and amide residues are cooperatively oriented in the same direction to result in asymmetric hydrogen-bonding belts. Unique circular dichroism (CD) bands are induced in the absorption wavelength ranges of the macrocyclic skeleton, caused by a chirality transmission from their chiral urea termini through hexyl spacers in the self-folded conformation. On the other hand, urea-functionalized resorcinarenes with a longer dodecyl spacer do not show such unique CD bands on the macrocycle, because of their weaker propensity for hydrogen bond formation. The characteristic CD bands of the urea-functionalized self-folding macrocycles disappeared upon complexation with anions such as chloride and bromide, reflecting breaking of the intramolecular hydrogen-bonding belts.     

Sequential nucleophilic substitution on halogenated triazines, pyrimidines, and purines: a novel approach to cyclic peptidomimetics.

A novel concept for the synthesis of macrocyclic peptidomimetics which incorporate heteroaromatic units is reported. The method involves sequential SNAr reactions of orthogonally protected amino groups of peptides and other linear oligomers on halogenated heterocycles such as 2,4,6-trichloro[1,3,5]triazine, 2,4,6-trichloropyrimidine, 4,6-dichloro-5-nitropyrimidine, and 2,6,8-trichloro-7-methylpurine. The scope of this novel solid-phase approach was systematically evaluated by means of the SPOT-synthesis methodology on planar cellulose membranes. Besides the question of the accessibility of different ring sizes and the compatibility with protecting groups of commonly used amino acids, the applicability of the technique toward different halogenated heteroaromatics and peptidomimetics was studied. It was found that the procedure is well suited to assemble a wide variety of cyclic peptidomimetics differing in both size (11- to 37-membered rings) and chemical nature of the assembled backbones.     

Hydrogen-bonding dynamics in aqueous solutions of amides and acids: monomer, dimer, trimer, and polymer

Hydrogen-bonding dynamics in aqueous solutions of series of amides and acids have been investigated by means of femtosecond Raman-induced Kerr effect spectroscopy and ab initio quantum chemistry calculation. The amides and acids studied here are acetamide, 1,3-propanedicarboxamide, 1,3,5-pentanetricaroxamide, polyacrylamide with Mw=1500, acetic acid, 1,3-propanedicarboxylic acid, 1,3,5-pentanetricarboxylic acid, and poly(acrylic acid) with Mw=2000. The femtosecond damped transient feature for aqueous amide solutions, which arises from the intermolecular hydrogen bonds of amide and water, becomes clearer with the larger molecular weight of amide. A characteristic vibrational band at about 100 cm(-1) is assigned as the hydrogen-bonding vibrational mode and the ab initio quantum chemistry calculation result indicates that at least two waters, which make up the hydrogen-bonding network with amide, are necessary for this mode. The hydrogen-bonding vibrational mode at about 100 cm(-1) in aqueous amide solutions shifts to the higher frequency with the larger molecular weight amide in consequence of the stronger intermolecular interaction between amide and water. The evidence likely comes from the stronger hydrophobic interaction for polymer than oligomers and monomer. In the picosecond time region, an extra slow relaxation process with a time constant of about 60 ps has been found in the aqueous polymer solutions. The relaxation is assigned as a local motion of the constitutional repeat unit of polymers from comparison with monomer and oligomers.     

Novel ester linked glycosyl amino acids: convenient building blocks for the synthesis of glycopeptide libraries

The completely orthogonally protected aspartic acid derivative FmocAsp(OBn)O^tBu is readily synthesized on a large scale. Deprotection of the β-carboxylic acid allows coupling to various sugar derivatives via free hydroxyl groups to produce novel glycosyl amino acids. Subsequent deprotection of either the α-acid or nitrogen is achieved cleanly to allow elaboration into an oligopeptide, whilst selective deprotection of PMB protected sugar hydroxyls is also readily achievable. Such novel glycosyl amino acid building blocks may be useful for the combinatorial synthesis of novel glycopeptide libraries.